Gather extra dependencies, homogeneize extra imports

pyproject.toml

@@ -17,9 +17,7 @@ cufinufft = ["cufinufft<2.3", "cupy-cuda12x"]
 finufft = ["finufft"]
 pynfft = ["pynfft2>=1.4.3; python_version < '3.12'", "numpy>=2.0.0; python_version < '3.12'"]
 pynufft = ["pynufft"]
-io = ["pymapvbvd"]
-smaps = ["scikit-image"]
-sampling = ["pywavelets", "scikit-learn"]
+extra = ["pymapvbvd", "scikit-image", "scikit-learn", "pywavelets"]
 autodiff = ["torch"]
 
 

src/mrinufft/extras/smaps.py

@@ -149,8 +149,15 @@ def low_frequency(
     """
     # defer import to later to prevent circular import
     from mrinufft import get_operator
-    from skimage.filters import threshold_otsu, gaussian
-    from skimage.morphology import convex_hull_image
+    try:
+        from skimage.filters import threshold_otsu, gaussian
+        from skimage.morphology import convex_hull_image
+    except ImportError as err:
+        raise ImportError(
+            "The scikit-image module is not available. Please install "
+            "it along with the [extra] dependencies "
+            "or using `pip install scikit-image`."
+        ) from err
 
     k_space, samples, dc = _extract_kspace_center(
         kspace_data=kspace_data,

src/mrinufft/io/siemens.py

@@ -60,6 +60,12 @@ def read_siemens_rawdat(
             "The mapVBVD module is not available. Please install it using "
             "the following command: pip install pymapVBVD"
         ) from err
+    except ImportError as err:
+        raise ImportError(
+            "The mapVBVD module is not available. Please install "
+            "it along with the [extra] dependencies "
+            "or using `pip install pymapVBVD`."
+        ) from err
     twixObj = mapVBVD(filename)
     if isinstance(twixObj, list):
         twixObj = twixObj[-1]

src/mrinufft/operators/stacked.py

@@ -23,7 +23,6 @@
 try:
     import cupy as cp
     from cupyx.scipy import fft as cpfft
-
 except ImportError:
     CUPY_AVAILABLE = False
 

src/mrinufft/trajectories/sampling.py

@@ -4,16 +4,10 @@
 import numpy.fft as nf
 import numpy.linalg as nl
 import numpy.random as nr
-from sklearn.cluster import BisectingKMeans, KMeans
 from tqdm.auto import tqdm
 
 from .utils import KMAX
 
-try:
-    import pywt as pw
-except ImportError:
-    pw = None
-
 
 def sample_from_density(
     nb_samples, density, method="random", *, dim_compensation="auto"
@@ -59,7 +53,15 @@ def sample_from_density(
        "Variable density sampling with continuous trajectories."
        SIAM Journal on Imaging Sciences 7, no. 4 (2014): 1962-1992.
     """
-    rng = nr.default_rng()
+    try:
+        from sklearn.cluster import BisectingKMeans, KMeans
+    except ImportError as err:
+        raise ImportError(
+            "The scikit-learn module is not available. Please install "
+            "it along with the [extra] dependencies "
+            "or using `pip install scikit-learn`."
+        ) from err
+
 
     # Define dimension variables
     shape = np.array(density.shape)
@@ -80,6 +82,7 @@ def sample_from_density(
         density = density / np.sum(density)
 
     # Sample using specified method
+    rng = nr.default_rng()
     if method == "random":
         choices = rng.choice(
             np.arange(max_nb_samples),
@@ -259,11 +262,14 @@ def create_chauffert_density(shape, wavelet_basis, nb_wavelet_scales, verbose=Fa
        In 2013 IEEE 10th International Symposium on Biomedical Imaging,
        pp. 298-301. IEEE, 2013.
     """
-    if pw is None:
+    try:
+        import pywt
+    except ImportError as err:
         raise ImportError(
-            "The PyWavelets package must be installed "
-            "as an additional dependency for this function."
-        )
+            "The PyWavelets module is not available. Please install "
+            "it along with the [extra] dependencies "
+            "or using `pip install pywavelets`."
+        ) from err
 
     nb_dims = len(shape)
     indices = np.indices(shape).reshape((nb_dims, -1)).T
@@ -330,11 +336,14 @@ def create_fast_chauffert_density(shape, wavelet_basis, nb_wavelet_scales):
        In 2013 IEEE 10th International Symposium on Biomedical Imaging,
        pp. 298-301. IEEE, 2013.
     """
-    if pw is None:
+    try:
+        import pywt
+    except ImportError as err:
         raise ImportError(
-            "The PyWavelets package must be installed "
-            "as an additional dependency for this function."
-        )
+            "The PyWavelets module is not available. Please install "
+            "it along with the [extra] dependencies "
+            "or using `pip install pywavelets`."
+        ) from err
 
     nb_dims = len(shape)